I have images of a fluorescence cytoplasmic protein in cells. In each image, I want to identify the whole cells and the organelles inside the cells; the organelles are darker because they don’t contain the tagged protein.
As I understand it, the traditional pipelines identify the primary objects first, i.e. the organelles, and then identify the secondary objects - the whole cells. However, identifying the organelles is a hard task because of differences in contrast between organelles and cytoplasm in different cells (there are different expression levels of the tagged protein). It would probably be easier to identify the cells first and then changing the contrast for each cell when trying to identify the organelles that it contains.
Are there modules that could be used to create such a pipeline, which identifies secondary objects first and then identifies primary objects contained in them?